As the Defiant crew survey the task ahead of them, Sisko prepares his strategy: groups of Federation attack fighters will make strafing runs at the blockade, focusing their fire only on the Cardassian starships. Nog is at a loss, and Garak explains that Sisko is hoping to provoke the Cardassians into breaking formation and opening a hole in the Dominion lines. It is the only chance the Federation has of reaching Deep Space 9 before the minefield is taken down. As they prepare to attack, O'Brien and Bashir quote from Tennyson's "The Charge of the Light Brigade", something which only makes a nervous Nog even more agitated. Finally, Sisko orders the attack fighters forward, and the battle is joined.

The Cardassians stand their ground after the fighters' first run, so Sisko orders the second and third waves forward.

On the station, safely back from the front line, Dukat, Damar, Weyoun, and the Female Changeling survey the developing battle. Dukat recognizes Sisko's strategy almost immediately, but instead of holding their ground, he explains to the Female Changeling that he plans to give Sisko his opening, and then use it to envelop him. As for the minefield, Dukat promises that it will be down in eight hours, something Weyoun says he will hold Dukat to. As the Founder and her Vorta commander leave, Damar sneers at their arrogance and egotism. Dukat chides him that the Dominion are their allies – for now. Damar then raises his concern that Federation-loyal elements may seek to sabotage the station again, hoping to damage or disable Terok Nor before the minefield is deactivated. Damar suggests that they be arrested until the battle is over. Rather than agitate the Bajorans, Dukat suggests that they merely be "held for questioning." However, Dukat firmly rejects Damar's suggestion that Ziyal be likewise detained, insisting that she is loyal to him and to Cardassia.

In Quark's, said "elements" – Kira, Jake and Leeta – are discussing the battle. Contradicting reports range from the two fleets slugging it out to the Federation fleet being completely annihilated. Kira suggests cutting off power to the main computer with a bomb, but before they can fully flesh out their plan – with unhelpful remarks from Quark – Damar arrives to take them to the security office, leaving only Quark behind, uncertain as to what to do.

Sisko continues to press the Cardassians – the ninth wave of fighters proves just as ineffective as the previous eight. But Dukat is now prepared to spring his trap. He orders half a dozen squadrons to pursue the next group of attacking ships, pulling them out of formation. As O'Brien and Garak note that a hole in the Dominion lines has been opened, Dax and Sisko note the position of two Galor-class starships moving into cross-fire positions, and realize that Dukat is luring them into a trap. But Sisko says this may be their only opportunity to break through, and orders the fleet to advance, detailing two wings of Galaxy-class starships to engage the Galors, and "All other ships, head for that opening. Anyone who gets through doesn't stop until they reach Deep Space Nine." The Federation fleet leaps forward, weapons blazing, and the two Galors are quickly dispatched. The Defiant, flanked by two Miranda-class starships, heads into the heart of the blockade fleet, taking multiple hits. The battle descends into a frantic melee as Dominion starships close around the Starfleet vessels and begin jamming fleet communications with a rotating EM pulse. Sisko's orders cannot get out to their intended recipients.

Dukat and Weyoun confer

Back on the station, Dukat is already pouring a toast in his office to what he considers their inevitable victory, and begins musing aloud on how best to administer the conquered systems of the Federation and the Klingons. Weyoun is much more pessimistic – noting that there are still five hours remaining before the Dominion reinforcements can come through the wormhole. He is likewise preoccupied with the formidable logistical task of occupying such a large swath of conquered territory as Dukat is considering. He concludes that the center of the inevitable resistance against Dominion occupation will be Earth, which is why it makes sense to eradicate its entire population. Dukat objects to such a measure as unnecessary; in his mind, the truest form of victory is to leave your enemy alive, so that they can see the error of their ways in resisting in the first place – "to force them to acknowledge your greatness." Weyoun asks, "Then you kill them?" and Dukat concedes, "only if it's necessary." Savoring his drink, Dukat's thoughts turn to the Occupation of Bajor and he says his one regret is that the Bajorans never saw him for what he really was: a protector, not a dictator, who shepherded them, rather than oppressed them. Dukat adds that Sisko, for all his perceptiveness, shares this unjust lack of respect for Dukat. Weyoun, contemplating that Dukat actually believes what he's saying, is both amused and fascinated by his egotism and self-delusion.

The Majestic and the Sitak are lost

The Female Changeling talks to Odo, regaling him with their success in the battle so far. He cannot share her sense of vindication, when people he used to consider his friends are fighting and dying. She retorts that they are only Solids, and that the Link means more. Odo isn't sure, and she realizes the reason behind his indecision – Kira and his feelings for her. The Female Changeling mentions Kira's arrest, and that she is to be put to death, so that Odo can regain the clarity she had attempted to provide. Odo is horrified, and turns away from her. She notes that Odo cannot help her, or any of his friends. It is too late for them.

The Defiant remains in the center of the battle, as its two Miranda escorts (USS Majestic and USS Sitak) are blown away by a concerted assault. Communications are restored, but the enemy numbers are too great. Garak wonders if it's time to cloak and run, but O'Brien says the cloaking device is fried. Seeing four Jem'Hadar attack ships directly ahead, Sisko orders the Defiant to fight its way through.

Destroying one fighter, the Defiant is pursued by the remaining three. Aft shields are down, forward shields are failing, and the cloaking device is off-line. Sisko orders all power to weapons. Just then, a fleet of Klingon starships emerges from the blinding light of the system's sun, hammering into the Dominion fleet. Worf contacts the Defiant and apologizes for being late – convincing Gowron to spare ships for the mission was not easy. With the Klingons reinforcing the assault, a real opening has appeared in the enemy lines, and the Defiant weaves its way through the battle, emerging alone in the wake of an exploding Jem'Hadar battle cruiser. With the rest of the fleet pinned down and three hours remaining before the detonation of the minefield, Sisko gives the command to set a course for Terok Nor at maximum warp.

Aboard the station, Weyoun orders pursuit, but Dukat notes that the station's defenses are more than enough to deal with one small starship, and Sisko's attack is nothing less than suicidal.

Quark and Ziyal attempt to free the Resistance

Meanwhile, Quark grabs Ziyal in her quarters, and asks her if she knows how to make hasperat soufflé. Ziyal is intrigued. The two then go to the security office, and attempt to take the soufflé to Kira. The Cardassian on guard is suspicious, and begins to disassemble the meal – only to be stopped by a hypospray wielded by Ziyal.

In the holding cells, Rom contemplates his imminent execution – with ninety minutes remaining, he expects to be dead two hours after (following a lengthy speech by Dukat and victory party with cake). Just then, Quark and Ziyal enter, Quark armed with a pair of Cardassian disruptors. He tells the two Jem'Hadar guards not to move, then demands they open the cells. Ziyal points out the flaw in his request, and as Quark restates his order, the Jem'Hadar raise their weapons. Acting on instinct, Quark fires first, killing both soldiers. Stunned, Quark can only stand and watch as Ziyal takes down the force field, and frees the Resistance members. Grabbing the guards' weapons, Kira and Rom plan to sabotage the main computer, and tell the rest of them to hide.

The Female Changeling continues to try and persuade Odo to link with her, only to be interrupted by Weyoun informing them of the escape. He recommends they go to Ops, where they will be safer, but Odo states he will remain behind.

Kira and Rom head for the main computer and attempt to shut down the power systems, pursued by Dominion forces. Pinned down in a cargo bay, Rom reacts in surprise at the sound of Bajoran phaser fire. Kira is at a loss to explain why Dominion forces would use Bajoran weapons, but when the shooting stops seconds later, she looks out and sees who had actually been using them – Odo has assembled his security force, and outflanked the enemy. As he escorts them to an access conduit, Kira asks why he changed his mind – Odo notes that the Link was paradise, but he isn't quite ready for paradise yet.

The Defiant is closing on the station – a mere eleven minutes away, cutting it a little close, O'Brien notes. Rom works frantically at the main computer core, Kira sitting helplessly watching. As she asks how the work is going, Rom realizes he won't make it in time. Kira suggests cutting power to the station's weapons array instead – without weapons, the minefield cannot be detonated, at least not before the Defiant can get there. Rom resumes his work. In space, the battle has begun to turn the way of the Allies. The Klingons have outflanked the Dominion blockade fleet, and their lines are starting to crumble. Dukat is undeterred – with the minefield about to be taken down, thousands of ships wait on the other side to reinforce their position. His only hope is that the Defiant arrives in time for Sisko to see it.

And his wish may be coming true. Dax suggests to Sisko that he might want to come up with an alternate plan. Rom is severing the final connections to the ODN relays just as Damar neutralizes the last mine leaving the field ready for detonation. Dukat gives the order just as Rom severs the last connection.

The minefield detonates

With a brilliant flash, the array of mines is wiped out. Rom was too late, and the Defiant too. Sisko and his crew watch in horror as the shock wave from the detonations blossoms around the station. He orders Dax to enter the wormhole – one last hopeless stand against the Dominion fleet. As the Female Changeling communicates to the Dominion reinforcements, Damar detects the approaching Defiant, and Weyoun gives the order to destroy her. But Rom's work has been successful, and the station's weapons are off-line. The Defiant enters the wormhole.

Sisko orders the ship to a halt – all power diverted to weapons and forward shields – as the Jem'Hadar fleet is seen on the viewscreen. The crew silently prepare themselves for the inevitable, when Sisko is suddenly pulled into the realm of the Prophets. They challenge his decision to end "the game" – they cannot allow him to die. Sisko tells them that the only way for them to save his life is to prevent the Jem'Hadar fleet from entering the Alpha Quadrant. The Prophets dismiss his demands – they are not concerned with corporeal matters, but Sisko rounds on them. What about Bajor? Their influence over that world is entirely a corporeal matter – and Bajor will be destroyed if the Dominion reinforcements arrive. "You want to be gods? Then be gods!" He tells them the only thing that can save him and Bajor now is a miracle. The Prophets agree, but note that a penance must be exacted for Sisko's interference. The Sisko is of Bajor, as the Prophets are, but he will find no rest there – he will follow a different path. Before he can find out what they mean, Sisko is returned to the Defiant, as the Dominion fleet enters weapons range.

Suddenly, the Jem'Hadar vessels are enveloped in waves of energy, and disappear completely. At first, O'Brien believes the ships have cloaked, but Dax cannot detect any neutrino emissions. The ships are just... gone.

On Terok Nor, Damar watches in horror as the Defiant emerges from the wormhole alone. Dukat tells him not to worry, their reinforcements must be right behind her... and the wormhole closes again, leaving him agape. Damar, checking the surrounding space and the Dominion's Gamma Quadrant listening posts, reports, stunned, that the reinforcements are nowhere to be found. The Defiant opens fire on the still-defenseless station. With weapons still offline, Damar announces that two hundred Allied ships have broken through their lines and are heading for the station; Weyoun orders an evacuation. The Female Changeling orders the Dominion forces to fall back to Cardassian space, noting the war will apparently take longer than expected. Dukat remains completely aghast at his sudden change in fortune, and his slim grasp on reality begins to crumble. As Damar organizes the evacuation, Dukat's sole thought is with Ziyal – he must find her. Sisko lets the Dominion forces evacuate – the Defiant is in no shape to stop them. Bashir relays a message from the USS Cortez – the Dominion forces are in full retreat. Smiling, Sisko gives the order for the fleet to rendezvous – at Deep Space 9.

Sisko returns to Deep Space 9

A disheveled and distraught Dukat wanders the Promenade, searching for Ziyal. Weyoun and the Female Changeling depart the station – Weyoun asks if Odo will be joining them; the Female Changeling says no, but it is only a matter of time. With one final look at his lost prize, Weyoun enters the airlock. Dukat has reached the habitat ring, and finds Ziyal looking for him. Dukat wants her to come back to Cardassia with him – she's all he cares about, all he has. But Ziyal doesn't want to leave. Dukat is insistent, the enemy is on its way; Ziyal says that they aren't her enemy – she's one of them, she helped Kira and the others escape. She belongs here on the station, and bids him goodbye. As she leaves, she turns back to tell Dukat she loves him – only to be shot by an overhearing Damar. Shattered by grief, Dukat runs to his dying daughter and tells her he forgives her, angrily shoving aside Damar as he tries to get him to leave.

Dukat, driven mad

The last Dominion ship has been routed, Starfleet has returned to Deep Space Nine, and Sisko sets foot upon his home once more to a cheering crowd of Bajorans and happily reunites with Jake. Martok arrives just afterward, noting that Sisko has won his wager with him – a barrel of bloodwine for the first of them to step aboard the station. Worf and Dax are reunited, and O'Brien and Bashir are too – with Quark's holosuites. Nog relates his promotion to his father and Leeta, remarking that this makes him Rom's superior officer. As Garak searches the Promenade, Sisko asks after Kira. The Major is in the Infirmary – with Ziyal. Garak reacts, and heads for the medical facility, finding Kira standing over the young woman's body. He remarks that he could never figure out why she loved him, and now he never will.

Dukat is still aboard the station, a shattered wreck of a man. Babbling to himself and an illusory Ziyal, he is helped out of a holding cell by Odo, handing Sisko's baseball to him as he does. Sisko regards the object for a moment, as Dukat is led away.

"Cannon to the right of them, Cannon to the left of them, Cannon in front of them, Volley'd and thunder'd."
"Storm'd at with shot and shell, Boldly they rode and well, Into the Jaws of Death, Into the mouth of hell... Rode the six hundred."
"Whatever it is you two are reciting, I wish you'd stop!"

"We didn't defeat the Federation by being cautious."
"We haven't defeated it yet. And even if we do, it's only the beginning. Holding onto a prize as vast as the Federation isn't going to be easy. It's going to require an enormous number of ships, a massive occupation army, and constant vigilance."
"I look forward to it!"

- Dukat and Weyoun

"A true victory is to make your enemies see they were wrong to oppose you in the first place. To force them to acknowledge your greatness!"
"Then you kill them?"
"Only if it's necessary."

- Dukat and Weyoun

"There are people out there...fighting, dying...people who used to be my friends."
"They're Solids, Odo – you must remember that."
"I know...but they still mean something to me!"
"The Link means more."
"That's what I keep telling myself...but somehow I can't quite believe it!"

- Odo and the Female Changeling

"Any other ships make it?"
"No, sir."

- Sisko and Nog, on the Defiant's bridge after it broke through the front lines

"Uh, Chief? How does that poem end?"
"You don't want to know."

- Garak and O'Brien, as Sisko orders the Defiant to enter the wormhole to confront the Dominion reinforcements alone

"Any questions?"
"I could ask why?"
"I don't think there's time to explain it – besides, I...think you know the answer."
"What about the link?"
"The link...was paradise. But it appears I'm not ready for paradise."

- Odo and Kira, after Odo and his men ambush the Jem'Hadar

"What about Bajor? You can't tell me Bajor doesn't concern you. You've sent the Bajorans Orbs, and Emissaries...you've even encouraged them to create an entire religion around you! You even told me once that you were 'Of Bajor' – so don't you tell me, you're not concerned with corporeal matters!...I don't want to see Bajor destroyed. Neither do you – but we all know that's exactly what's going to happen if the Dominion takes over the Alpha Quadrant!...You say you don't want me to sacrifice my life – well FINE! Neither do I. You want to be gods? Then BE gods!...I need a miracle. Bajor needs a miracle...STOP THOSE SHIPS!!!"

- Sisko, convincing the Prophets to stop the Dominion

"Victory was within our grasp...! (...) Bajor... The Federation... The Alpha Quadrant... All lost!"

- Dukat, starting to break down

"Time to start packing!"

- Weyoun, when the Federation fleet begins to retake Terok Nor

"She loved you."
"I could never figure out why. I guess I never will."

- Kira and Garak, regarding Ziyal

"What about Odo – is he coming with us?"
(Sadly)"No...but he will join us one day – it's only a matter of time."

When the multi-episode arc was originally conceived, it was four episodes long, but once the writers started to develop ideas and decide where specific plot points needed to go and how things needed to develop, Ira Steven Behr changed it to a five-episode arc. For a considerable amount of time it remained a five-episode narrative, even getting to the stage where titles were being assigned. At that point, "Favor the Bold" was the final episode, and encompassed the final space battle, the rebellion on Deep Space 9 and the Federation's reacquisition of the station. After Behr and co-writer Hans Beimler began to run into trouble trying to fit everything into forty-four minutes however, Behr realized that one episode simply could not contain all that was needed to finish off such a large narrative arc. As such, he and Beimler basically split the last episode into two, and began to fill it out, thus creating a mini two-parter to conclude the overall six-parter. (Star Trek: Deep Space Nine Companion)

That the six-episode arc was extremely successful is illustrated by Ira Steven Behr; "ultimately everyone agreed that it was tremendously successful, and one of the best things the show ever did." Similarly, that it marked an important turning point for the show is hinted at by Hans Beimler, "It showed us the possibilities and the excitement that could be garnered, and in the end, we liked it so much that we decided to do the ten-episode arc at the end of the series." (Star Trek: Deep Space Nine Companion)

This episode contains the largest battle ever seen in Star Trek, topping "The Way of the Warrior", which itself had topped "The Die is Cast". It is also the first Star Trek episode where CGI is used exclusively. Being the first episode where the battle scenes were entirely done in CGI, the producers realized that this was a massive project for television and quickly decided to split the workload between Digital Muse and Foundation Imaging. The latter was tasked with digitizing the alien ships, while the former would handle those Federation ships that were not digitized yet. The animation of the battle itself was for the first half handled by Digital Muse; Foundation did the second half (with the USS Defiant breaking through the lines and the arrival of the Klingons). Visual effects supervisor David Stipes explains that traditionally, scenes like this were done on the sound stage with models via motion-control rigs, but that was not an option this time, due to the immensity of the battle; "the problem is that motion control is about shooting one ship at a time, one pass at a time. There was just no way we could have done it. We just didn't have enough time or money." (Star Trek: Deep Space Nine Companion)

This episode marks the death of Tora Ziyal (Melanie Smith) and the onset of Gul Dukat's descent into madness, however, Ira Steven Behr maintains that Dukat was well on his way to madness long before Ziyal's death' "The difference between Dukat and someone like Sisko – it's one of the ultimate differences of this show. A healthy human being like Sisko knows himself. That doesn't mean he doesn't have limitations. It doesn't mean he doesn't make mistakes. But he knows himself. Dukat is a totally self-deluded person. He's a deeply, deeply screwed up Cardassian who doesn't understand his own motives. He loved Ziyal, but like the true sociopathic personality he is, he wasn't above using her, or lying to her." (Star Trek: Deep Space Nine Companion) Dukat's motives, his madness and his delusions would next be addressed in the episode "Waltz".

Of the death of Ziyal itself, Hans Beimler says, "We understood the ramifications on all the characters. We'd built up her relationship with Garak. The girl who always told the truth had fallen in love with the guy who never tells the truth – or all of the truth. It made for a nice tragic love story, and her death served to motivate Garak in his future actions." (Star Trek: Deep Space Nine Companion)

The Prophets' description of Sisko's life as "the game" is a reference back to the series premiere. There, Sisko explains linear existence to the Prophets using a baseball game as a metaphor. They also referred to 'the game' when explaining to Quark why they had taken away Zek's greed in the third season episode "Prophet Motive" – because he wanted to know the outcome of the game before it was over.

When Sisko says to the Prophets, "You once told me you were of Bajor", he is referring to the fourth season episode "Accession". After "Emissary" and "Accession", this episode represents Sisko's third visit to the Prophets.

At the end of the episode, Sisko gets the Prophets to help him, but there is a price to pay; an idea with many mythic and biblical precursors. Hans Beimler says, "It's tragic hero stuff. A hero takes on things for others, but doesn't necessarily find any peace himself in the result." In relation to this, Ira Steven Behr compares Sisko to Moses (who guides his people to the Promised Land, but who isn't allowed to enter himself) and Ethan Edwards (the John Wayne character in the 1956John Ford film The Searchers who reunites his family but cannot enter the house with them). (Star Trek: Deep Space Nine Companion)

When this show aired, there were some criticisms of it having a deus ex machina ending, something which infuriated Ira Steven Behr; "I felt it was the perfect next step in the evolution of the relationship between Sisko and the Prophets that began in the pilot. Hearing people refer to it as some dopey deus ex machina is really annoying because I would think they'd give us more credit for being on the ball. We didn't have to end it like that, we chose to end it like that. Because we wanted to say that there was something going on here. And ultimately, that would lead to our finding out that Sisko is part-Prophet. They wouldn't have done this for just anyone. This was the man going out into the wilderness and demanding God to interfere, to do something for crying out loud. The corporeal characters had done so much in the episode; surely they'd earned the help of the gods." (Star Trek: Deep Space Nine Companion)

The story document for this episode was distributed around Paramount with a typo on the cover – instead of being entitled "Sacrifice of Angels", it was entitled "Sacrifice of Angles". Ira Steven Behr has jokingly said that he prefers the 'Angles' title. (Star Trek: Deep Space Nine Companion)

Dukat's strategy – deliberately opening a hole in the Dominion-Cardassian lines, hoping to draw the enemy in and then envelop them – is similar to the successful strategy used by Hannibal at the Battle of Cannae on Earth in the third century BC. It is interesting that Bashir is the one to point out the trap; Alexander Siddig later portrayed Hannibal in a made-for-TV film.

In the novel Unity, the Jem'Hadar soldiers of the missing fleet attack the neural parasite mother creature.

In Star Trek Online, the missing Dominion fleet plays a critical role in the Featured Episode series, "The 2800", where it is returned to the Alpha Quadrant 34 years after the war ended, and proceeds to capture Deep Space 9.